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Table 3 Variants in risk-associated genes

From: A neurodegenerative disease landscape of rare mutations in Colombia due to founder effects

Gene

Coding change

dbSNP/ClinVar

Classification

ExAC

1000G

CADD

Local ancestry

ABCA7

c.2T>C

rs1347920426

PTV (nonsense)

.

.

24.9

Native American

c.236A>C (p.Asn79Thr)

rs377401443

SD

4.16E-05

.

24.5

African

c.1180_1190del (p.Leu396fs)

rs567222111

PTV (frameshift)

0.0005

0.0022

.

African

c.1531G>T (p.Glu511*)

rs374932832

PTV (nonsense)

7.60E-05

.

39

African

c.1776G>T (p.Trp592Cys)

SCV001751545

SD

.

.

26

African

c.2124_2130del (p.Glu709fs)+

rs547447016

PTV (frameshift)

0.0024

0.0006

.

European

c.2194C>T (p.Gln732*)

rs1030634619

PTV (nonsense)

.

.

36

European

c.2552+11_2552+58del

rs1178315251

PTV (splice)

.

.

.

African

c.2611G>C (p.Asp871His)

rs139251928

SD

0.0004

0.0014

24.8

African

c.3781delC (p.Pro1261fs)

SCV001751546

PTV (frameshift)

  

.

Native American

c.4208delT (p.Leu1403fs)

rs538591288

PTV (frameshift)

0.0011

.

.

European

c.4465C>T (p.Arg1489*)

rs753664323

PTV (nonsense)

6.66E-05

.

39

European

c.4886C>T (p.Ser1629Leu)+

rs184590335

SD

0.0012

0.0006

35

Native American

c.4895C>T (p.Pro1632Leu)

rs143083561

SD

0.0002

0.0006

34

African

c.5302delC (p.Leu1768fs)

rs1348650979

PTV (frameshift)

.

.

.

Native American

c.5463+2T>C

rs374611445

PTV (splice)

2.81E-05

.

23.7

European

c.5794C>T (p.Arg1932C)

rs114787084

SD

0.0002

0.0006

34

African

SORL1

c.994C>T (p.Arg332Trp)

rs772110877

SD

5.77E-05

.

35

European

c.1432G>C (p.Ala478Pro)

SCV001751547

SD

.

.

28.2

European

c.1496C>T (p.Ser499Leu)

rs764032259

SD

8.24E-06

.

35

European

c.2200G>A (p.Asp734Asn)

rs148430425

SD

0.0011

.

34

European

c.2230C>T (p.Arg744*)

rs1050845490

PTV (nonsense)

.

.

39

European

c.2710C>T (p.Arg904Trp)

rs148966249

SD

4.12E-05

2.00E-04

33

Native American

c.3679G>T (p.Gly1227Cys)

rs1765488318

SD

.

.

34

European

c.4520C>T (p.Pro1507Leu)

rs1308522330

SD

.

.

26.2

Undetermined

c.6550G>A (p.Ala2184Thr)

rs369618646

SD

4.16E-05

.

34

African

TREM2

c.140G>A (p.Arg47His)+

rs75932628

SD

0.0021

0.002

33

European

c.469C>T (p.His157Tyr)+

rs2234255

SD

0.0036

0.0028

23.1

Native American

NM_001271821

c.287C>A (p.Thr96Lys)

c.572G>A(p.Trp191*)

c.632T>C (p.Leu211Pro)

rs2234253

rs2234258

rs2234256

PTV (nonsense)

   

African

c.594G>A (p.Trp198*)

rs1765488318

PTV (nonsense)

.

.

39

Undetermined

ADAM10

c.510G>C (p.Gln170His)+

rs61751103

SD

0.0012

0.0012

19.17

European

  1. PTV protein truncating variant, SD strictly damaging, ExAC ExAC database minor allelic frequency. CADD corresponds to the Phred score. Variants denoted with a + were identified in homozygous states. GenBank transcripts for each gene can be found in Additional file 4: Table S3